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Radecki AA, Fantasia-Davis A, Maldonado JS, Mann JW, Sepulveda-Camacho S, Morosky P, Douglas J, Vargas-Rodriguez O. Coexisting bacterial aminoacyl-tRNA synthetase paralogs exhibit distinct phylogenetic backgrounds and functional compatibility with Escherichia coli. IUBMB Life 2024. [PMID: 39417753 DOI: 10.1002/iub.2920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 09/26/2024] [Indexed: 10/19/2024]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are universally essential enzymes that synthesize aminoacyl-tRNA substrates for protein synthesis. Although most organisms require a single aaRS gene for each proteinogenic amino acid to translate their genetic information, numerous species encode multiple gene copies of an aaRS. Growing evidence indicates that organisms acquire extra aaRS genes to sustain or adapt to their unique lifestyle. However, predicting and defining the function of repeated aaRS genes remains challenging due to their potentially unique physiological role in the host organism and the inconsistent annotation of repeated aaRS genes in the literature. Here, we carried out comparative, phylogenetic, and functional studies to determine the activity of coexisting paralogs of tryptophanyl-, tyrosyl-, seryl-, and prolyl-tRNA synthetases encoded in several human pathogenic bacteria. Our analyses revealed that, with a few exceptions, repeated aaRSs involve paralogous genes with distinct phylogenetic backgrounds. Using a collection of Escherichia coli strains that enabled the facile characterization of aaRS activity in vivo, we found that, in almost all cases, one aaRS displayed transfer RNA (tRNA) aminoacylation activity, whereas the other was not compatible with E. coli. Together, this work illustrates the challenges of identifying, classifying, and predicting the function of aaRS paralogs and highlights the complexity of aaRS evolution. Moreover, these results provide new insights into the potential role of aaRS paralogs in the biology of several human pathogens and foundational knowledge for the investigation of the physiological role of repeated aaRS paralogs across bacteria.
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Affiliation(s)
- Alexander A Radecki
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Ariana Fantasia-Davis
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Juan S Maldonado
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Joshua W Mann
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | | | - Pearl Morosky
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Jordan Douglas
- Department of Physics, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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Bennett ZD, Brunold TC. Non-standard amino acid incorporation into thiol dioxygenases. Methods Enzymol 2024; 703:121-145. [PMID: 39260993 PMCID: PMC11391102 DOI: 10.1016/bs.mie.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Thiol dioxygenases (TDOs) are non‑heme Fe(II)‑dependent enzymes that catalyze the O2-dependent oxidation of thiol substrates to their corresponding sulfinic acids. Six classes of TDOs have thus far been identified and two, cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), are found in eukaryotes. All TDOs belong to the cupin superfamily of enzymes, which share a common β‑barrel fold and two cupin motifs: G(X)5HXH(X)3-6E(X)6G and G(X)5-7PXG(X)2H(X)3N. Crystal structures of TDOs revealed that these enzymes contain a relatively rare, neutral 3‑His iron‑binding facial triad. Despite this shared metal-binding site, TDOs vary greatly in their secondary coordination spheres. Site‑directed mutagenesis has been used extensively to explore the impact of changes in secondary sphere residues on substrate specificity and enzymatic efficiency. This chapter summarizes site-directed mutagenesis studies of eukaryotic TDOs, focusing on the tools and practicality of non‑standard amino acid incorporation.
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Affiliation(s)
- Zachary D Bennett
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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Douglas J, Bouckaert R, Carter CW, Wills P. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Res 2024; 52:558-571. [PMID: 38048305 PMCID: PMC10810186 DOI: 10.1093/nar/gkad1160] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
How genetic information gained its exquisite control over chemical processes needed to build living cells remains an enigma. Today, the aminoacyl-tRNA synthetases (AARS) execute the genetic codes in all living systems. But how did the AARS that emerged over three billion years ago as low-specificity, protozymic forms then spawn the full range of highly-specific enzymes that distinguish between 22 diverse amino acids? A phylogenetic reconstruction of extant AARS genes, enhanced by analysing modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades, resulting in a total of 36 families of AARS catalytic domains. Small structural modules that differentiate one AARS family from another played pivotal roles in discriminating between amino acid side chains, thereby expanding the genetic code and refining its precision. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that were not synthesised until later in the evolution of the code. The most probable evolutionary route for an emergent amino acid type to establish a place in the code was by recruiting older, less specific AARS, rather than adapting contemporary lineages. This process, retrofunctionalisation, differs from previously described mechanisms through which amino acids would enter the code.
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Affiliation(s)
- Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
- School of Computer Science, The University of Auckland, New Zealand
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA
| | - Peter R Wills
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
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Jindal A, Patil N, Bains A, Sridhar K, Stephen Inbaraj B, Tripathi M, Chawla P, Sharma M. Recent Trends in Cereal- and Legume-Based Protein-Mineral Complexes: Formulation Methods, Toxicity, and Food Applications. Foods 2023; 12:3898. [PMID: 37959017 PMCID: PMC10649166 DOI: 10.3390/foods12213898] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Minerals play an important role in maintaining human health as the deficiency of these minerals can lead to serious health issues. To address these deficiencies, current research efforts are actively investigating the utilization of protein-mineral complexes as eco-friendly, non-hazardous, suitable mineral fortifiers, characterized by minimal toxicity, for incorporation into food products. Thus, we reviewed the current challenges in incorporating the cereal-legume protein-inorganic minerals complexes' structure, binding properties, and toxicity during fortification on human health. Moreover, we further reviewed the development of protein-mineral complexes, characterization, and their food applications. The use of inorganic minerals has been associated with several toxic effects, leading to tissue-level toxicity. Cereal- and legume-based protein-mineral complexes effectively reduced the toxicity, improved bone mineral density, and has antioxidant properties. The characterization techniques provided a better understanding of the binding efficiency of cereal- and legume-based protein-mineral complexes. Overall, understanding the mechanism and binding efficiency underlying protein-mineral complex formation provided a novel insight into the design of therapeutic strategies for mineral-related diseases with minimal toxicity.
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Affiliation(s)
- Aprajita Jindal
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara 144411, India; (A.J.); (N.P.)
| | - Nikhil Patil
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara 144411, India; (A.J.); (N.P.)
| | - Aarti Bains
- Department of Microbiology, Lovely Professional University, Phagwara 144411, India
| | - Kandi Sridhar
- Department of Food Technology, Karpagam Academy of Higher Education (Deemed to Be University), Coimbatore 641021, India
| | | | - Manikant Tripathi
- Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya 224001, India
| | - Prince Chawla
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara 144411, India; (A.J.); (N.P.)
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Thoma B, Powner MW. Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water. J Am Chem Soc 2023; 145:3121-3130. [PMID: 36700882 PMCID: PMC9912261 DOI: 10.1021/jacs.2c12497] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Why life encodes specific proteinogenic amino acids remains an unsolved problem, but a non-enzymatic synthesis that recapitulates biology's universal strategy of stepwise N-to-C terminal peptide growth may hold the key to this selection. Lysine is an important proteinogenic amino acid that, despite its essential structural, catalytic, and functional roles in biochemistry, has widely been assumed to be a late addition to the genetic code. Here, we demonstrate that lysine thioacids undergo coupling with aminonitriles in neutral water to afford peptides in near-quantitative yield, whereas non-proteinogenic lysine homologues, ornithine, and diaminobutyric acid cannot form peptides due to rapid and quantitative cyclization that irreversibly blocks peptide synthesis. We demonstrate for the first time that ornithine lactamization provides an absolute differentiation of lysine and ornithine during (non-enzymatic) N-to-C-terminal peptide ligation. We additionally demonstrate that the shortest lysine homologue, diaminopropionic acid, undergoes effective peptide ligation. This prompted us to discover a high-yielding prebiotically plausible synthesis of the diaminopropionic acid residue, by peptide nitrile modification, through the addition of ammonia to a dehydroalanine nitrile. With this synthesis in hand, we then discovered that the low basicity of diaminopropionyl residues promotes effective, biomimetic, imine catalysis in neutral water. Our results suggest diaminopropionic acid, synthesized by peptide nitrile modification, can replace or augment lysine residues during early evolution but that lysine's electronically isolated sidechain amine likely provides an evolutionary advantage for coupling and coding as a preformed monomer in monomer-by-monomer peptide translation.
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Hazra B, Prasad M, Roy R, Tarafdar PK. The microenvironment and p Ka perturbation of aminoacyl-tRNA guided the selection of cationic amino acids. Org Biomol Chem 2021; 19:8049-8056. [PMID: 34505850 DOI: 10.1039/d1ob00798j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proteinogenic lysine (Lys) and arginine (Arg) have multiple methylene groups between α-carbon and the terminal charged centre. Why nature did not select ornithine (Orn), 2,4-diamino butyric acid (Dab) and 2,3-diamino propionic acid (Dpr) with fewer methylene groups in the side chain remains an important question! The propensity of aminoacyl-tRNA (aa-tRNA) model substrates towards self-degradation via intramolecular lactamization was studied using UV spectroscopy and 1H-NMR titration, which showed that Lys and Arg remain stable, and Orn and Dab cyclize to lactam. Hydrophobicity-assisted surface mediated model peptide formation highlighted that the microenvironment and pKa perturbation led to poor regioselectivity (α-amine vs. terminal amine) in Dpr and other non-proteinogenic analogues. The α-selectivity became even poorer in the presence of phosphate, making them ill-suited for peptide synthesis. Superior regioselectivity of the Lys aa-tRNA model substrate suggests that the extra methylene bridge helped nature to separate the microenvironments of the α-amine and ε-amine to synthesize the peptide backbone.
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Affiliation(s)
- Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, PIN-741246, India.
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, PIN-741246, India.
| | - Rajat Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, PIN-741246, India.
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, PIN-741246, India.
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